I am wondering if with this new version, whether those settings should be changed.I am getting great results with the new version, most of my screens are drawn on Canvases and the improvement is like night and day.But having a few odd cases where screens aren't refreshing as expected so now wondering if I should be turning off these old settings.

The rule of thumb is set everything to False. If you have scrolling regions that look like they are tearing or not refreshing correctly then try a Control.Refresh(false). For example when using a scrollbar to move a a container, place a Refresh(false) after you adjust the Top or Scroll (for canvas). You should only need to use Transparent or DoubleBuffer in special cases.